[phenixbb] Memory and CPU usage

Pavel Afonine pafonine at lbl.gov
Mon Jul 30 09:58:50 PDT 2012

Hi Jon,

you can find the answer without wasting time on guesswork... Take a few 
extreme cases from PDB (big model, many reflections, tricky space 
group), and run them from the command line:

phenix.refine model.pdb data.mtz ordered_solvent=true --show-process-info

The log file should contain memory usage throughout the run. Look for 
the max memory intake in the last record (towards the end of log file). 
This will give you an idea about how much memory you may need.


On 7/22/12 4:31 AM, Jon Agirre wrote:
> Dear Nat and Pavel,
> thank you so much for your explanations. Assuming that the 8 in Nat's 
> formula provides conversion to bytes, it is not such a big RAM 
> requirement. I guess most virus structures should be approachable with 
> an 8GB machine.
> About the CPU, I think I'm going to invest in a quad-core. I feel 
> quite comfortable in command line and I don't have fear paralelizing 
> existing code.
> Thanks again,
> Jon
> 2012/7/21 Pavel Afonine <pafonine at lbl.gov <mailto:pafonine at lbl.gov>>
>         But the resolution_factor is inconsistent - for the FFT structure
>         factors calculation (which is unavoidable), we are definitely
>         using
>         1/3 (I assume for speed reasons).  For most of the other optional
>         tasks like rotamer correction and filling missing F-obs, it's 1/4.
>     Yes, we use 1/3 for structure factors and gradients calculations,
>     and 1/4 in map calculation if the map is going to be used for
>     things like water picking, real-space refinement, etc. This is
>     intentional.
>     Pavel
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>     phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
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> -- 
> Jon Agirre, PhD
> Biophysics Unit (CSIC-UPV/EHU)
> http://www.ehu.es/jon.agirre
> +34656756888
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